Lists (8)
AI learning
clinical analysis
Analysis using TCGA and other datasetsgenome models
AI models for human genomeML interpretability
Research into the inner workings of an AI modelnetwork analysis
Analysis of networks using python or Rsenescence scoring and markers
Repos describing a list of senescence markers or methods to score senescent cells.Single cell statistical analysis
Statistical methods to test the embeddings, clustering, and DE genesTranscription factor network
Computational tools for transcription factor network (TF-target genes) reconstruction using bulk and single-cell datasets on GithubStars
Semi-parametric approach for the inference of gene regulatory networks from time series of expression data
A Granger Causality and Mediation Framework for Inferring Direct Causal Networks in Time-Series Proteomics
R toolkit for inference, visualization and analysis of cell-cell communication from single-cell and spatially resolved transcriptomics
A customized PyTorch-BigGraph (PBG) package for "simba", modified from https://github.com/facebookresearch/PyTorch-BigGraph
CellNavi is a deep learning framework designed to predict genes driving cellular transitions.
Python library for finding the optimal transformation(s) that makes two matrices as close as possible to each other.
Error-controlled interaction discovery in machine learning models
Notebooks to follow along with "Deep Learning for Biology" Chapters 2 to 6.
Implements *CellAnnotator (aka *CAT/starCAT), annotating scRNA-Seq with predefined gene expression programs
scooby: Modeling multi-modal genomic profiles from DNA sequence at single-cell resolution.
Toolkit for training hyenaDNA-based autoregressive language models on DNA sequences.
Biological foundation modeling from molecular to genome scale
open source interpretability platform 🧠
inference of transcription factor activity at the single cell level
Gene regulatory network containing signed transcription factor-target gene interactions
Graph-linked unified embedding for single-cell multi-omics data integration
A Python package with which to find network motifs in complex networks and to analyze a growing list of network-motif related stuff.
Network Reverse Engineering through AP inference of Mutual Information
A Cellular Regulatory Network-Aware Transcriptomics Foundation Model
This is a repository for the LinkedIn Learning course Build Advanced Charts in R
CellWalkR: An R Package for integrating single-cell and bulk data to resolve regulatory elements
Python package for creating and visualizing interactive network graphs.
karyoploteR - An R/Bioconductor package to plot arbitrary data along the genome
This API provides programmatic access to the AlphaGenome model developed by Google DeepMind.